The exit status of the task that caused the workflow execution to fail was: null.
The full error message was:
Error executing process > 'NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM (SRR11452476)'
Caused by:
Process `NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM (SRR11452476)` terminated for an unknown reason -- Likely it has been terminated by the external system
Command executed:
samtools \
merge \
--threads 1 \
\
--reference human_g1k_v37_decoy.fasta \
SRR11452476.recal.cram \
1/SRR11452476_GL000222.recal.cram 2/SRR11452476_18_1-78077248.recal.cram 3/SRR11452476_GL000200.recal.cram 4/SRR11452476_GL000193.recal.cram 5/SRR11452476_6_1-171115067.recal.cram 6/SRR11452476_15_1-102531392.recal.cram 7/SRR11452476_22_1-51304566.recal.cram 8/SRR11452476_GL000225.recal.cram 9/SRR11452476_9_1-141213431.recal.cram 10/SRR11452476_21_1-48129895.recal.cram 11/SRR11452476_14_1-107349540.recal.cram 12/SRR11452476_X_1-155270560.recal.cram 13/SRR11452476_Y_1-59373566.recal.cram 14/SRR11452476_GL000192.recal.cram 15/SRR11452476_hs37d5_1-35477943.recal.cram 16/SRR11452476_GL000194.recal.cram 17/SRR11452476_GL000212.recal.cram 18/SRR11452476_GL000215.recal.cram 19/SRR11452476_GL000216.recal.cram 20/SRR11452476_GL000219.recal.cram 21/SRR11452476_GL000205.recal.cram 22/SRR11452476_GL000224.recal.cram 23/SRR11452476_NC_007605_1-171823.recal.cram 24/SRR11452476_GL000195.recal.cram 25/SRR11452476_GL000217.recal.cram 26/SRR11452476_13_1-115169878.recal.cram 27/SRR11452476_GL000223.recal.cram 28/SRR11452476_GL000199.recal.cram 29/SRR11452476_16_1-90354753.recal.cram 30/SRR11452476_17_1-81195210.recal.cram 31/SRR11452476_2_1-243199373.recal.cram 32/SRR11452476_8_1-146364022.recal.cram 33/SRR11452476_4_1-191154276.recal.cram 34/SRR11452476_3_1-198022430.recal.cram 35/SRR11452476_11_1-135006516.recal.cram 36/SRR11452476_10_1-135534747.recal.cram 37/SRR11452476_7_1-159138663.recal.cram 38/SRR11452476_20_1-63025520.recal.cram 39/SRR11452476_12_1-133851895.recal.cram 40/SRR11452476_5_1-180915260.recal.cram 41/SRR11452476_19_1-59128983.recal.cram 42/SRR11452476_1_1-249250621.recal.cram
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM":
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS
Command exit status:
-
Command output:
(empty)
Command wrapper:
ls: SRR11452476.recal.bam: No such file or directory
ls: *.csi: No such file or directory
Work dir:
/input/data/work/dc/728b91c307e04b744144b3944601df
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
nextflow run /input/sarek -profile test_full -c /experiments/experiment/sarek/nextflow.config -c /experiments/experiment/nextflow_cws.config -c /experiments/experiment/nextflow_nfs.configc2275107d1eafbc01b31ce8cf99ccbd721bcbfa1-8a99-4785-bd98-2b7987412e29These plots give an overview of the distribution of resource usage for each process.
This table shows information about each task in the workflow. Use the search box on the right to filter rows for specific values. Clicking headers will sort the table by that value and scrolling side to side will reveal more columns.